def get_common_parser(include_pathway=True):
parser = MyParser(fromfile_prefix_chars='@')
group = parser.add_mutually_exclusive_group()
group.add_argument("-v",
"--verbose",
action="count",
default=0,
help="increase output verbosity")
group.add_argument("-q",
"--quiet",
action="count",
default=0,
help="decrease output verbosity")
parser.add_argument('--dataset',
default='both',
help='Default: both',
choices=known_datasets)
if include_pathway:
parser.add_argument('--pathway',
default='serotonin',
help='Default: serotonin'
) #, choices=['all'] + cfg.pathways.keys())
parser.add_argument(
'--from_age',
help=
'Use only data points with larger ages than this. Default: all ages',
choices=dct_ages.keys())
parser.add_argument('--scaling',
help='What scaling to use for ages. Default: log',
default='log',
choices=allowed_scaler_names())
parser.add_argument('--shuffle',
help='Shuffle the y-values of the data',
action='store_true')
parser.add_argument('-s',
'--shape',
help='The shape to use for fitting. Default: sigslope',
default='sigslope',
choices=allowed_shape_names())
parser.add_argument(
'--sigma_prior',
help='Prior to use for 1/sigma when fitting. Default: normal',
default='normal',
choices=get_allowed_priors(is_sigma=True))
parser.add_argument(
'--priors',
help='Priors to use for theta when fitting. Default: sigslope80',
default='sigslope80',
choices=get_allowed_priors())
return parser
NOT_USED = (None,)
parser = get_common_parser()
parser.add_argument('--part', help='Compute only part of the genes. format: <k>/<n> e.g. 1/4. (k=1..n)')
parser.add_argument('--html', nargs='?', metavar='DIR', default=NOT_USED, help='Create html for the fits. Optionally override output directory.')
parser.add_argument('--mat', action='store_true', help='Save the fits also as matlab .mat file.')
parser.add_argument('--text', action='store_true', help='Save the theta parameters also to a text file (spline only).')
parser.add_argument('--correlations', action='store_true', help='Use correlations between genes for prediction')
parser.add_argument('--correlations_part', help='Compute only part of the correlations. format: <k>/<n> e.g. 1/4. (k=1..n)')
parser.add_argument('--onset', action='store_true', help='Show onset times and not R2 scores in HTML table (sigmoid only)')
parser.add_argument('--dont_show_change_dist', action='store_true', help="Don't show change distribution in the figures (only relevant for sigmoids and together with --html)")
parser.add_argument('--no_legend', action='store_true', help="Don't show the legend in the figures (only relevant together with --html)")
parser.add_argument('--change_dist', action='store_true', help='Compute change distributions and related measures (sigmoid only)')
parser.add_argument('--exons_layout', action='store_true', default = False, help='Adjust plotting and html layout to exon-level data')
parser.add_argument('--exons_same_scale',action='store_true',default = False, help='Set y axis range to be the same for all exons in multi-exons subplots')
parser.add_argument('--exons_plots_from_series',action='store_true',default = False, help='Build multi-exons plots from series plots')
parser.add_argument('--plots_scaling',default = 'none', help = 'What scaling to use for expression levels when plotting. Currently affects only exons plots. Default: none.', choices=allowed_scaler_names())
args = parser.parse_args()
if args.part is not None and args.mat:
abort('--mat cannot be used with --part')
is_sigmoid = args.shape in ['sigmoid','sigslope']
if args.correlations:
if args.part:
abort('--correlations cannot be used with --part')
if args.mat:
abort('--correlations not compatible with --mat')
if args.correlations_part:
if not args.correlations:
abort('--correlations_part cannot should not used with also specifying --correlations')
if args.html != NOT_USED:
plt.scatter(scores1, scores2, alpha=0.5)
plt.plot([-1, 1], [-1, 1],'k--')
plt.xlim(-1,1)
plt.ylim(-1,1)
ttl1 = r'Comparison of scores using {} vs. {}'.format(fitter1.shape,fitter2.shape)
ttl2 = r'{}, {}'.format(data1.name, data1.pathway)
plt.title('\n'.join([ttl1, ttl2]), fontsize=cfg.fontsize)
plt.xlabel('R2 for {}'.format(fitter1.shape), fontsize=cfg.fontsize)
plt.ylabel('R2 for {}'.format(fitter2.shape), fontsize=cfg.fontsize)
return fig
if __name__ == '__main__':
disable_all_warnings()
parser = get_common_parser()
parser.add_argument('--shape2', required=True, help='The shape to compare against', choices=allowed_shape_names())
parser.add_argument('--scaling2', help='The scaling used when fitting shape2. Default: none', choices=allowed_scaler_names())
parser.add_argument('--sigma_prior2', help='Prior to use for 1/sigma when fitting shape2. Default: None', choices=get_allowed_priors(is_sigma=True))
parser.add_argument('--priors2', help='The priors used for theta when fitting shape2. Default: None', choices=get_allowed_priors())
parser.add_argument('--filename', help='Where to save the figure. Default: results/comparison.png')
parser.add_argument('--show', help='Show figure and wait before exiting', action='store_true')
parser.add_argument('--ndiffs', type=int, default=5, help='Number of top diffs to show. Default=5.')
args = parser.parse_args()
data1, fitter1 = process_common_inputs(args)
data2 = get_data_from_args(args.dataset, args.pathway, args.from_age, args.scaling2, args.shuffle)
fitter2 = get_fitter_from_args(args.shape2, args.priors2, args.sigma_prior2)
fits1 = get_all_fits(data1,fitter1)
fits2 = get_all_fits(data2,fitter2)
print_diff_points(data1,fitter1,fits1, data2,fitter2,fits2, args.ndiffs)
def get_common_parser(include_pathway=True):
parser = MyParser(fromfile_prefix_chars='@')
group = parser.add_mutually_exclusive_group()
group.add_argument("-v", "--verbose", action="count", default=0, help="increase output verbosity")
group.add_argument("-q", "--quiet", action="count", default=0, help="decrease output verbosity")
parser.add_argument('--dataset', default='both', help='Default: both', choices=known_datasets)
if include_pathway:
parser.add_argument('--pathway', default='serotonin', help='Default: serotonin') #, choices=['all'] + cfg.pathways.keys())
parser.add_argument('--from_age', help='Use only data points with larger ages than this. Default: all ages', choices=dct_ages.keys())
parser.add_argument('--scaling', help='What scaling to use for ages. Default: none', default='none', choices=allowed_scaler_names())
parser.add_argument('--shuffle', help='Shuffle the y-values of the data', action='store_true')
parser.add_argument('-s', '--shape', help='The shape to use for fitting. Default: sigslope', default='sigslope', choices=allowed_shape_names())
parser.add_argument('--sigma_prior', help='Prior to use for 1/sigma when fitting. Default: None', choices=get_allowed_priors(is_sigma=True))
parser.add_argument('--priors', help='Priors to use for theta when fitting. Default: None', choices=get_allowed_priors())
return parser